Alignments for a candidate for paaK in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Escherichia coli BW25113

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate 15520 b1398 phenylacetyl-CoA ligase (NCBI)

Query= SwissProt::P76085
         (437 letters)



>FitnessBrowser__Keio:15520
          Length = 437

 Score =  888 bits (2294), Expect = 0.0
 Identities = 437/437 (100%), Positives = 437/437 (100%)

Query: 1   MITNTKLDPIETASVDELQALQTQRLKWTLKHAYENVPMYRRKFDAAGVHPDDFRELSDL 60
           MITNTKLDPIETASVDELQALQTQRLKWTLKHAYENVPMYRRKFDAAGVHPDDFRELSDL
Sbjct: 1   MITNTKLDPIETASVDELQALQTQRLKWTLKHAYENVPMYRRKFDAAGVHPDDFRELSDL 60

Query: 61  RKFPCTTKQDLRDNYPFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARS 120
           RKFPCTTKQDLRDNYPFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARS
Sbjct: 61  RKFPCTTKQDLRDNYPFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARS 120

Query: 121 LRAAGGSPKDKIHVAYGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDFQPDM 180
           LRAAGGSPKDKIHVAYGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDFQPDM
Sbjct: 121 LRAAGGSPKDKIHVAYGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDFQPDM 180

Query: 181 IMVTPSYCLNLIEELERQLGGDASGCSLRVGVFGAEPWTQAMRKEIERRLGITALDIYGL 240
           IMVTPSYCLNLIEELERQLGGDASGCSLRVGVFGAEPWTQAMRKEIERRLGITALDIYGL
Sbjct: 181 IMVTPSYCLNLIEELERQLGGDASGCSLRVGVFGAEPWTQAMRKEIERRLGITALDIYGL 240

Query: 241 SEVMGPGVAMECLETTDGPTIWEDHFYPEIVNPHDGTPLADGEHGELLFTTLTKEALPVI 300
           SEVMGPGVAMECLETTDGPTIWEDHFYPEIVNPHDGTPLADGEHGELLFTTLTKEALPVI
Sbjct: 241 SEVMGPGVAMECLETTDGPTIWEDHFYPEIVNPHDGTPLADGEHGELLFTTLTKEALPVI 300

Query: 301 RYRTRDLTRLLPGTARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEIVKFEHLSPHYQL 360
           RYRTRDLTRLLPGTARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEIVKFEHLSPHYQL
Sbjct: 301 RYRTRDLTRLLPGTARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEIVKFEHLSPHYQL 360

Query: 361 EVNRRGHLDSLSVKVELKESSLTLTHEQRCQVCHQLRHRIKSMVGISTDVMIVNCGSIPR 420
           EVNRRGHLDSLSVKVELKESSLTLTHEQRCQVCHQLRHRIKSMVGISTDVMIVNCGSIPR
Sbjct: 361 EVNRRGHLDSLSVKVELKESSLTLTHEQRCQVCHQLRHRIKSMVGISTDVMIVNCGSIPR 420

Query: 421 SEGKACRVFDLRNIVGA 437
           SEGKACRVFDLRNIVGA
Sbjct: 421 SEGKACRVFDLRNIVGA 437


Lambda     K      H
   0.320    0.137    0.411 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 825
Number of extensions: 23
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 437
Length of database: 437
Length adjustment: 32
Effective length of query: 405
Effective length of database: 405
Effective search space:   164025
Effective search space used:   164025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate 15520 b1398 (phenylacetyl-CoA ligase (NCBI))
to HMM TIGR02155 (paaF: phenylacetate-CoA ligase (EC 6.2.1.30))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02155.hmm
# target sequence database:        /tmp/gapView.31346.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02155  [M=422]
Accession:   TIGR02155
Description: PA_CoA_ligase: phenylacetate-CoA ligase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.4e-242  790.5   0.0   1.6e-242  790.4   0.0    1.0  1  lcl|FitnessBrowser__Keio:15520  b1398 phenylacetyl-CoA ligase (N


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15520  b1398 phenylacetyl-CoA ligase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  790.4   0.0  1.6e-242  1.6e-242       1     422 []      11     432 ..      11     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 790.4 bits;  conditional E-value: 1.6e-242
                       TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavprekvvr 79 
                                     e++s+del+alq++rlk+++k+ayenvp+yr++fdaagv+pdd++elsdl+kfp+t+k+dlrdnypfd++avp+e+vvr
  lcl|FitnessBrowser__Keio:15520  11 ETASVDELQALQTQRLKWTLKHAYENVPMYRRKFDAAGVHPDDFRELSDLRKFPCTTKQDLRDNYPFDTFAVPMEQVVR 89 
                                     899**************************************************************************** PP

                       TIGR02155  80 vhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGatvvpisGGqtek 158
                                     +hassGttGkptvv+ytq+d+d+w+++varslraaGG+++d++h+ayGyGlftGGlG+hyGae+lGatv+p+sGGqtek
  lcl|FitnessBrowser__Keio:15520  90 IHASSGTTGKPTVVGYTQNDIDNWANIVARSLRAAGGSPKDKIHVAYGYGLFTGGLGAHYGAERLGATVIPMSGGQTEK 168
                                     ******************************************************************************* PP

                       TIGR02155 159 qvqliqdfkpdiiavtpsyilalleelkrlg.idpedislkvailGaepwteamrkelearlgikaldiyGlseviGpG 236
                                     q+qli+df+pd+i+vtpsy+l+l+eel+r+   d++ +sl+v+++Gaepwt+amrke+e+rlgi+aldiyGlsev+GpG
  lcl|FitnessBrowser__Keio:15520 169 QAQLIRDFQPDMIMVTPSYCLNLIEELERQLgGDASGCSLRVGVFGAEPWTQAMRKEIERRLGITALDIYGLSEVMGPG 247
                                     *****************************9769********************************************** PP

                       TIGR02155 237 vanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvfttltkealpviryrtrdltrllpgtartmrrmdkikG 315
                                     va+ec+et+dG++iwedhfypei++p++g++l+dGe+Gel+fttltkealpviryrtrdltrllpgtartmrrmd+i+G
  lcl|FitnessBrowser__Keio:15520 248 VAMECLETTDGPTIWEDHFYPEIVNPHDGTPLADGEHGELLFTTLTKEALPVIRYRTRDLTRLLPGTARTMRRMDRISG 326
                                     ******************************************************************************* PP

                       TIGR02155 316 rsddllilrGvnvfptqleevllkldklsphyqleltreGaldeltlkvelkdesaalrlleqksllakkiekkikaev 394
                                     rsdd+li+rGvnvfp+qlee ++k+++lsphyqle++r+G+ld+l++kvelk es+ + ++eq+++++++++++ik++v
  lcl|FitnessBrowser__Keio:15520 327 RSDDMLIIRGVNVFPSQLEEEIVKFEHLSPHYQLEVNRRGHLDSLSVKVELK-ESSLTLTHEQRCQVCHQLRHRIKSMV 404
                                     ****************************************************.8888889******************* PP

                       TIGR02155 395 gvsvdvelvepgslerseGkakrvvdkr 422
                                     g+s+dv++v++gs++rseGka+rv+d+r
  lcl|FitnessBrowser__Keio:15520 405 GISTDVMIVNCGSIPRSEGKACRVFDLR 432
                                     **************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (437 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.33
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources